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Deal with older vcf formats and samples with missing data #147

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Deal with older vcf formats and samples with missing data #147

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6 changes: 4 additions & 2 deletions pypgx/api/genotype.py
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Original file line number Diff line number Diff line change
Expand Up @@ -619,11 +619,13 @@ def call_genotypes(alleles=None, cnv_calls=None):

if alleles is not None and cnv_calls is not None:
if set(alleles.data.index) != set(cnv_calls.data.index):
raise ValueError('SampleTable[Alleles] and '
'SampleTable[CNVCalls] have different samples')
_diff = set(cnv_calls.data.index)- set(alleles.data.index)
print(_diff)
print("Are missing and will be droped")
if alleles.metadata['Gene'] != cnv_calls.metadata['Gene']:
raise ValueError('Found two different target genes')
df = pd.concat([alleles.data, cnv_calls.data], axis=1)
df = df.dropna()
gene = alleles.metadata['Gene']
assembly = alleles.metadata['Assembly']
elif alleles is not None and cnv_calls is None:
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6 changes: 6 additions & 0 deletions pypgx/api/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1299,6 +1299,12 @@ def prepare_depth_of_coverage(
exclude=exclude
).to_regions()


regions = [
item for item in regions
if item.split(':')[0].isdigit() or item.split(':')[0] in {'X', 'Y'}
]

cf = pycov.CovFrame.from_bam(bams, regions=regions, zero=True)

if bed:
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